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https://www.readbyqxmd.com/read/29149730/divergence-of-insulin-superfamily-ligands-receptors-and-igf-binding-proteins-in-marine-versus-freshwater-stickleback-evidence-of-selection-in-known-and-novel-genes
#1
Tim Pellissier, Hend Al Nafea, Sara V Good
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29149451/transcriptional-alterations-in-hereditary-and-sporadic-nonfunctioning-pancreatic-neuroendocrine-tumors-according-to-genotype
#2
Xavier M Keutgen, Suresh Kumar, Sudheer Gara, Myriem Boufraqech, Sunita Agarwal, Ralph H Hruban, Naris Nilubol, Martha Quezado, Richard Finney, Maggie Cam, Electron Kebebew
BACKGROUND: Nonfunctioning pancreatic neuroendocrine tumors (NFPanNETs) may be sporadic or inherited because of germline mutations associated with von Hippel-Lindau disease (VHL) or multiple endocrine neoplasia type 1 (MEN1). The clinical behavior of NFPanNETs is difficult to predict, even in tumors of the same stage and grade. The authors analyzed genotype-specific patterns of transcriptional messenger RNA (mRNA) levels of NFPanNETs to understand the molecular features that determine PanNET phenotype...
November 17, 2017: Cancer
https://www.readbyqxmd.com/read/29149410/tctp-in-neuronal-circuitry-assembly
#3
Cláudio Gouveia Roque, Christine E Holt
Although tctp expression in many areas of the human brain was reported more than 15 years ago, little was known about how it functions in neurons. The early notion that Tctp is primarily expressed in mitotic cells, together with reports suggesting a relative low abundance in the brain, has perhaps potentiated this almost complete disregard for the study of Tctp in the context of neuron biology. However, recent evidence has challenged this view, as a number of independent genome-wide profiling studies identified tctp mRNA among the most enriched in the axonal compartment across diverse neuronal populations, including embryonic retinal ganglion cells...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/29149250/modeling-the-causal-role-of-dna-methylation-in-the-association-between-cigarette-smoking-and-inflammation-in-african-americans-a-2-step-epigenetic-mendelian-randomization-study
#4
Min A Jhun, Jennifer A Smith, Erin B Ware, Sharon L R Kardia, Thomas H Mosley, Stephen T Turner, Patricia A Peyser, Sung Kyun Park
The association between cigarette smoking and inflammation is well known. However, the biological mechanisms behind the association are not fully understood, particularly the role of DNA methylation, which is known to be affected by smoking. Using 2-step epigenetic Mendelian randomization, we investigated the role of DNA methylation in the association between cigarette smoking and inflammation. In 822 African Americans from the Genetic Epidemiology Network of Arteriopathy, phase 2 (Jackson, Mississippi; 2000-2005), study population, we examined the association of cigarette smoking with DNA methylation using single nucleotide polymorphisms identified in previous genome-wide association studies of cigarette smoking...
November 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29149221/dietary-protein-sources-differentially-affect-microbiota-mtor-activity-and-transcription-of-mtor-signaling-pathways-in-the-small-intestine
#5
Soumya K Kar, Alfons J M Jansman, Nirupama Benis, Javier Ramiro-Garcia, Dirkjan Schokker, Leo Kruijt, Ellen H Stolte, Johanna J Taverne-Thiele, Mari A Smits, Jerry M Wells
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.25 g) were randomly assigned to groups fed for four weeks with semi synthetic diets prepared with one of the following protein sources containing (300 g/kg as fed basis): soybean meal (SBM), casein, partially delactosed whey powder, spray dried plasma protein, wheat gluten meal and yellow meal worm...
2017: PloS One
https://www.readbyqxmd.com/read/29149188/orienting-the-causal-relationship-between-imprecisely-measured-traits-using-gwas-summary-data
#6
Gibran Hemani, Kate Tilling, George Davey Smith
Inference about the causal structure that induces correlations between two traits can be achieved by combining genetic associations with a mediation-based approach, as is done in the causal inference test (CIT). However, we show that measurement error in the phenotypes can lead to the CIT inferring the wrong causal direction, and that increasing sample sizes has the adverse effect of increasing confidence in the wrong answer. This problem is likely to be general to other mediation-based approaches. Here we introduce an extension to Mendelian randomisation, a method that uses genetic associations in an instrumentation framework, that enables inference of the causal direction between traits, with some advantages...
November 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29149178/drivers-of-genetic-diversity-in-secondary-metabolic-gene-clusters-within-a-fungal-species
#7
Abigail L Lind, Jennifer H Wisecaver, Catarina Lameiras, Philipp Wiemann, Jonathan M Palmer, Nancy P Keller, Fernando Rodrigues, Gustavo H Goldman, Antonis Rokas
Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence...
November 17, 2017: PLoS Biology
https://www.readbyqxmd.com/read/29148600/new-evidence-for-the-recent-divergence-of-devil-s-hole-pupfish-and-the-plausibility-of-elevated-mutation-rates-in-endangered-taxa
#8
Christopher H Martin, Sebastian Höhna
Saglam et al. (2016) recently argued that the Devil's Hole Pupfish (Cyprinodon diabolis), a conservation icon with the smallest known species range, was isolated 60 kya based on a new genomic dataset. If true, this would be a radically long timescale for any species to persist at population sizes less than 500 individuals, in contrast to conservation genetics theory. However, here we argue that their analyses and interpretation are inappropriate. They placed highly restrictive prior distributions on divergence times, which do not appropriately model the large uncertainty and result in removing nearly all uncertainty from their analyses, and chose among models by assuming that pupfishes exhibit human mutation rates...
November 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29148204/genome-wide-and-phenome-wide-approaches-to-understand-variable-drug-actions-in-electronic-health-records
#9
REVIEW
Jamie R Robinson, Joshua C Denny, Dan M Roden, Sara L Van Driest
No abstract text is available yet for this article.
November 17, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/29147930/snp-association-study-in-pms2-associated-lynch-syndrome
#10
Sanne W Ten Broeke, Fadwa A Elsayed, Lisa Pagan, Maran J W Olderode-Berends, Encarna Gomez Garcia, Hans J P Gille, Liselot P van Hest, Tom G W Letteboer, Lizet E van der Kolk, Arjen R Mensenkamp, Theo A van Os, Liesbeth Spruijt, Bert J W Redeker, Manon Suerink, Yvonne J Vos, Anja Wagner, Juul T Wijnen, E W Steyerberg, Carli M J Tops, Tom van Wezel, Maartje Nielsen
Lynch syndrome (LS) patients are at high risk of developing colorectal cancer (CRC). Phenotypic variability might in part be explained by common susceptibility loci identified in Genome Wide Association Studies (GWAS). Previous studies focused mostly on MLH1, MSH2 and MSH6 carriers, with conflicting results. We aimed to determine the role of GWAS SNPs in PMS2 mutation carriers. A cohort study was performed in 507 PMS2 carriers (124 CRC cases), genotyped for 24 GWAS SNPs, including SNPs at 11q23.1 and 8q23.3...
November 17, 2017: Familial Cancer
https://www.readbyqxmd.com/read/29147778/genome-wide-investigation-of-transcription-factors-provides-insights-into-transcriptional-regulation-in-plutella-xylostella
#11
Qian Zhao, Dongna Ma, Yuping Huang, Weiyi He, Yiying Li, Liette Vasseur, Minsheng You
Transcription factors (TFs), which play a vital role in regulating gene expression, are prevalent in all organisms and characterization of them may provide important clues for understanding regulation in vivo. The present study reports a genome-wide investigation of TFs in the diamondback moth, Plutella xylostella (L.), a worldwide pest of crucifers. A total of 940 TFs distributed among 133 families were identified. Phylogenetic analysis of insect species showed that some of these families were found to have expanded during the evolution of P...
November 16, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29147756/locus-and-gene-based-gwas-meta-analysis-identifies-new-diabetic-nephropathy-genes
#12
Mohammad Saeed
Objective Assimilation of SNPs Interacting in Synchrony (OASIS) is a locus-based clustering algorithm recently described that can potentially address false positives and negatives in genome-wide association studies (GWAS) of complex disorders. Diabetic nephropathy (DN) is incompletely understood due to a paucity of genes identified despite several GWAS. OASIS was applied to three DN dbGAP GWAS datasets (4725 subjects; 1.06 million SNPs). OASIS identified 19 DN genes which were verified using single variant replication in a standard association study and gene-based analysis using GATES...
November 16, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29147737/genetic-dissection-of-early-season-cold-tolerance-in-sorghum-genome-wide-association-studies-for-seedling-emergence-and-survival-under-field-and-controlled-environment-conditions
#13
Sebastian Parra-Londono, Karin Fiedler, Mareike Kavka, Birgit Samans, Silke Wieckhorst, Arndt Zacharias, Ralf Uptmoor
A QTL on sorghum chromosome SBI-06 putatively improves field emergence under low-temperature conditions. Low temperatures decisively limit seedling emergence and vigor during early growth of sorghum and, thus, strongly impair geographical expansion. To broaden sorghum cultivation to temperate regions, the establishment of cold-tolerant genotypes is a prioritized breeding goal. The present study aims at the quantification of seedling emergence and survival under chilling temperatures and the detection of marker-trait associations controlling temperature-related seedling establishment...
November 16, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29147069/expression-profiling-of-long-noncoding-rna-splice-variants-in-human-microvascular-endothelial-cells-lipopolysaccharide-effects-in-vitro
#14
Imran H Chowdhury, Hema P Narra, Abha Sahni, Kamil Khanipov, Casey L C Schroeder, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. We report on the expression profile of long noncoding (lnc) RNAs of human microvascular endothelial cells in response to LPS...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/29147026/leveraging-genome-characteristics-to-improve-gene-discovery-for-putamen-subcortical-brain-structure
#15
Chi-Hua Chen, Yunpeng Wang, Min-Tzu Lo, Andrew Schork, Chun-Chieh Fan, Dominic Holland, Karolina Kauppi, Olav B Smeland, Srdjan Djurovic, Nilotpal Sanyal, Derrek P Hibar, Paul M Thompson, Wesley K Thompson, Ole A Andreassen, Anders M Dale
Discovering genetic variants associated with human brain structures is an on-going effort. The ENIGMA consortium conducted genome-wide association studies (GWAS) with standard multi-study analytical methodology and identified several significant single nucleotide polymorphisms (SNPs). Here we employ a novel analytical approach that incorporates functional genome annotations (e.g., exon or 5'UTR), total linkage disequilibrium (LD) scores and heterozygosity to construct enrichment scores for improved identification of relevant SNPs...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146952/migrainomics-identifying-brain-and-genetic-markers-of-migraine
#16
REVIEW
Dale R Nyholt, David Borsook, Lyn R Griffiths
Migraine is one of the world's most prevalent and disabling disorders and imposes an enormous socioeconomic burden. The exact causes of migraine are unknown, and no recognizable diagnostic pathological changes have been identified. Specific identifiable markers of migraine would aid diagnosis and could provide insight into the pathogenesis of the condition, with the potential to direct development of new therapeutics. In the past few years, advances in neuroimaging and genetic studies have provided the most substantial progress towards the identification of markers...
November 17, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/29146897/gwas-for-male-pattern-baldness-identifies-71-susceptibility-loci-explaining-38-of-the-risk
#17
Nicola Pirastu, Peter K Joshi, Paul S de Vries, Marilyn C Cornelis, Paul M McKeigue, NaNa Keum, Nora Franceschini, Marco Colombo, Edward L Giovannucci, Athina Spiliopoulou, Lude Franke, Kari E North, Peter Kraft, Alanna C Morrison, Tõnu Esko, James F Wilson
Male pattern baldness (MPB) or androgenetic alopecia is one of the most common conditions affecting men, reaching a prevalence of ~50% by the age of 50; however, the known genes explain little of the heritability. Here, we present the results of a genome-wide association study including more than 70,000 men, identifying 71 independently replicated loci, of which 30 are novel. These loci explain 38% of the risk, suggesting that MPB is less genetically complex than other complex traits. We show that many of these loci contain genes that are relevant to the pathology and highlight pathways and functions underlying baldness...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145811/genome-wide-analysis-of-the-auxin-indoleacetic-acid-aux-iaa-gene-family-in-allotetraploid-rapeseed-brassica-napus-l
#18
Haitao Li, Bo Wang, Qinghua Zhang, Jing Wang, Graham J King, Kede Liu
BACKGROUND: Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known. RESULTS: In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes...
November 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29145809/genome-wide-characterization-and-expression-profiling-of-pdi-family-gene-reveals-function-as-abiotic-and-biotic-stress-tolerance-in-chinese-cabbage-brassica-rapa-ssp-pekinensis
#19
Md Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Gopal Saha, Manosh Kumar Biswas, Hoy-Taek Kim, Ill-Sup Nou
BACKGROUND: Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145743/novel-avenues-for-drug-discovery-in-diabetic-kidney-disease
#20
Matthew D Breyer, Matthias Kretzler
Diabetic kidney disease (DKD) has emerged as major cause of morbidity and mortality. After progressing to renal failure, over 70% of DKD patients are dead with five years. New treatments to slow this progression are desperately needed. Areas covered: This review highlights the current treatment options for people with DKD with a particular focus on angiotensin pathway blockade and the potential use of sodium glucose linked transporter 2 (SGLT2) inhibitors. These treatments are associated with an initial decrease in glomerular filtration rate (GFR) and albuminuria; there is also attention on renal hyperfiltration as therapeutic target...
November 16, 2017: Expert Opinion on Drug Discovery
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